st_all

Written by Aunoy Poddar July 21st, 2022

Process the puncta quantified raw data

current_file <- rstudioapi::getActiveDocumentContext()$path
output_file <- stringr::str_replace(current_file, '.Rmd', '.R')
knitr::purl(current_file, output = output_file)
file.edit(output_file)

Import packages and functions

library(Seurat)

Registered S3 methods overwritten by 'htmltools':
  method               from         
  print.html           tools:rstudio
  print.shiny.tag      tools:rstudio
  print.shiny.tag.list tools:rstudio
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio
Attaching SeuratObject

library(tictoc)
library(ggplot2)
library(patchwork)
library(pheatmap)
library(RColorBrewer)
library(tidyverse)

Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      
── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✔ tibble  3.1.8     ✔ dplyr   1.0.8
✔ tidyr   1.2.0     ✔ stringr 1.4.0
✔ readr   2.1.2     ✔ forcats 0.5.1
✔ purrr   0.3.4     
── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(gridExtra)

Attaching package: ‘gridExtra’

The following object is masked from ‘package:dplyr’:

    combine

library(png)
library(cowplot)

Attaching package: ‘cowplot’

The following object is masked from ‘package:patchwork’:

    align_plots

library(magick)

Linking to ImageMagick 6.9.10.23
Enabled features: fontconfig, freetype, fftw, lcms, pango, webp, x11
Disabled features: cairo, ghostscript, heic, raw, rsvg
Using 80 threads

library(scales)

Attaching package: ‘scales’

The following object is masked from ‘package:purrr’:

    discard

The following object is masked from ‘package:readr’:

    col_factor

Load the data

data_dir = '/home/aunoy/st/arc_profiling/st_analysis/hand_annotated_data/rethresholded'
meta_dir = '/home/aunoy/st/arc_profiling/st_analysis/hand_annotated_data/overlay'
output_dir_plot = '/home/aunoy/st/arc_profiling/st_analysis/results/plots'
output_dir_tbls = '/home/aunoy/st/arc_profiling/st_analysis/results/tables'

Merge both datasets and generate a metadata column that corresponds

to the cell

df_408 = data.frame()
for (file_name in list.files(data_dir)){
  print(file_name)
  if(grepl('164', file_name)){
    next
  }
  #if(grepl('408_TC', file_name) | grepl('408_vMS', file_name)){
  #  next
  #}
  df_to_append <- read.table(file.path(data_dir, file_name), sep = ',', header = TRUE)
  while(length(ind <- which(df_to_append$Image.Name == "")) > 0){
    df_to_append$Image.Name[ind] <- df_to_append$Image.Name[ind -1]
  }
  
  colnames(df_to_append) <- toupper(colnames(df_to_append))
  df_to_append <- df_to_append %>%
    mutate(area = strsplit(file_name, '.csv')[[1]])
  
  ## Add relative_XY_position
  
  if(!is_empty(df_408)){
    df_to_append <- df_to_append %>%
          dplyr::select(colnames(df_408))
  }
  df_408 <- rbind(df_408, df_to_append)
}

[1] "164_CC.csv"
[1] "164_MS_CC.csv"
[1] "164_MS_TC.csv"
[1] "164_TC.csv"
[1] "408_CC.csv"
[1] "408_dMS_TC.csv"
[1] "408_MS_CC.csv"
[1] "408_TC.csv"
[1] "408_vMS_TC.csv"

df_408$IMAGE.NAME = unlist(lapply(df_408$IMAGE.NAME, gsub, pattern='_Cluster', replacement=''))
df_408$IMAGE.NAME = unlist(lapply(df_408$IMAGE.NAME, gsub, pattern='[*]', replacement=''))
df_408$IMAGE.NAME = unlist(lapply(df_408$IMAGE.NAME, gsub, pattern='X', replacement=''))
df_408$IMAGE.NAME = unlist(lapply(df_408$IMAGE.NAME, gsub, pattern='L2_', replacement='L2-'))
df_408$IMAGE.NAME = unlist(lapply(df_408$IMAGE.NAME, gsub, pattern='-L2', replacement='_L2'))
df_408$IMAGE.NAME = unlist(lapply(df_408$IMAGE.NAME, gsub, pattern='Tc_12', replacement='TC_12'))
## Missing
df_408 = df_408[df_408$IMAGE.NAME != 'Layer1', ]
df_408 = df_408[df_408$IMAGE.NAME != 'TC_1', ]
df_408 = df_408[df_408$IMAGE.NAME != 'TC_18', ]
df_408 = df_408[df_408$IMAGE.NAME != 'TC_19', ]
#df_408$IMAGE.NAME = toupper(df_408$IMAGE.NAME)
unique(df_408$IMAGE.NAME)

 [1] "CC_Cortical1" "CC_Cortical2" "CC_L2-1"      "CC_L2-2"      "CC_L2-3"      "TC_2"         "TC_3"         "TC_4"         "TC_5"         "TC_6"        
[11] "TC_7"         "TC_8"         "TC_9"         "TC_10"        "CC_4"         "CC_5"         "CC_6"         "CC_7"         "CC_8"         "CC_9"        
[21] "CC_10"        "CC_11"        "CC_12"        "TC_16"        "TC_17"        "TC_20"        "TC_11"        "TC_12"        "TC_13"        "TC_14"       
[31] "TC_15"       

Order the images

unique(df_408$IMAGE.NAME)

 [1] "CC_Cortical1" "CC_Cortical2" "CC_L2-1"      "CC_L2-2"      "CC_L2-3"      "TC_2"         "TC_3"         "TC_4"         "TC_5"         "TC_6"        
[11] "TC_7"         "TC_8"         "TC_9"         "TC_10"        "CC_4"         "CC_5"         "CC_6"         "CC_7"         "CC_8"         "CC_9"        
[21] "CC_10"        "CC_11"        "CC_12"        "TC_16"        "TC_17"        "TC_20"        "TC_11"        "TC_12"        "TC_13"        "TC_14"       
[31] "TC_15"       

images_ordered = c('TC_20', 'TC_17', 'TC_16', 'TC_15', 'TC_14', 'TC_13', 'TC_12', 'TC_11', 'TC_10', 'TC_9', 'TC_8', 'TC_7', 'TC_6', 'TC_5',
                   'TC_4', 'TC_3', 'TC_2', 'CC_4', 'CC_5', 'CC_6', 'CC_7', 'CC_8', 'CC_9', 'CC_10', 'CC_11', 'CC_12', 'CC_L2-3', 'CC_L2-2', 'CC_L2-1', 'CC_Cortical1', 'CC_Cortical2')

x_horz = 1:length(images_ordered) * 35
y_horz = rep(0, length(images_ordered))
horz_embedding = data.frame()
df_408$X_horz = -1
df_408$Y_horz = -1
IMAGE_SIZE = 1024
## This is the size of an image in the global coordinate space
IMAGE_LEN = 25

images = list.files(meta_dir)
for(i in 1:length(images_ordered)){
    image_name = images_ordered[i]
    print(image_name)
    split_names = strsplit(image_name, '_')
    cortex = toupper(split_names[[1]][1])
    number = split_names[[1]][2]
    number_csv = paste0('_', number, '.csv')
    filename = images[grepl(cortex, images) & grepl(number_csv, images) & grepl('408', images)]
    coordinates = read.table(file.path(meta_dir, filename), sep = ',', header = TRUE)
    ## checked already that lists are equal, missing 1, 18, 19 for now, layer 1 and others
 
    ## so this is a little tricky, so need to get it right
    ## Remember, it is the top right that the coordinate is coming from, but
    ## the bottom right is the new coordinate space.
    ## so first when we get the original coordinate space, to set to relative
    ## of bottom would be the same X, but 1024 - Y
    
    ## push out the coordinates for better visualization
    #x_repelled <- (512 - coordinates$X_Coordinate_In_pixels)
    
    
    df_408[df_408$IMAGE.NAME == image_name, 'X_horz'] = (coordinates$X_Coordinate_In_pixels / 
                                                      IMAGE_SIZE * IMAGE_LEN) + y_horz[i]
    df_408[df_408$IMAGE.NAME == image_name, 'Y_horz'] = ((1024-coordinates$Y_Coordinate_In_pixels) / 
                                                      IMAGE_SIZE * IMAGE_LEN) + x_horz[i]
}

[1] "TC_20"
[1] "TC_17"
[1] "TC_16"
[1] "TC_15"
[1] "TC_14"
[1] "TC_13"
[1] "TC_12"
[1] "TC_11"
[1] "TC_10"
[1] "TC_9"
[1] "TC_8"
[1] "TC_7"
[1] "TC_6"
[1] "TC_5"
[1] "TC_4"
[1] "TC_3"
[1] "TC_2"
[1] "CC_4"
[1] "CC_5"
[1] "CC_6"
[1] "CC_7"
[1] "CC_8"
[1] "CC_9"
[1] "CC_10"
[1] "CC_11"
[1] "CC_12"
[1] "CC_L2-3"
[1] "CC_L2-2"
[1] "CC_L2-1"
[1] "CC_Cortical1"
[1] "CC_Cortical2"

We have the coordinates for 408_TC and others

rownames(df_408) = 1:nrow(df_408)
jy_408 = df_408 %>%
  dplyr::select(-c(area, IMAGE.NAME, X_horz, Y_horz)) %>%
  t() %>%
  CreateSeuratObject()

just set everything from below 1 in ratio to zero

jy_408 <- NormalizeData(jy_408, scale.factor = 1e5) ###

Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

normed = GetAssayData(jy_408, slot = 'data')
normed[normed < 3] = 0
jy_408 <- SetAssayData(jy_408, slot = 'data', normed)

jy_408 <- FindVariableFeatures(jy_408, selection.method = "vst")

Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

all.genes <- rownames(jy_408)
jy_408 <- ScaleData(jy_408, features = all.genes)

Centering and scaling data matrix

  |                                                                                                                                                            
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  |======================================================================================================================================================| 100%

jy_408 <- RunPCA(jy_408, approx = FALSE)

Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
PC_ 1 
Positive:  VIP, ASCL1, CXCR4, RELN, SATB2, MAF1, KIA0319, EMX1, GAD1, CXCL12 
       PAX6, DLX2, SST, PROX1, LHX6, NCAM1 
Negative:  DCX, TBR1, LRP8, SCGN, COUPTF2, EGFR, CXCL14, TSHZ1, GSX2, EOMES 
       SP8, NKX2.1, CALB2, CXCR7, DCDC2, VLDLR 
PC_ 2 
Positive:  TBR1, EOMES, KIA0319, DCDC2, LRP8, CALB2, DCX, SATB2, CXCL12, EGFR 
       EMX1, ASCL1, COUPTF2, PAX6, RELN, CXCR4 
Negative:  MAF1, TSHZ1, NKX2.1, SST, GAD1, DLX2, PROX1, SP8, GSX2, VIP 
       SCGN, LHX6, VLDLR, CXCL14, CXCR7, NCAM1 
PC_ 3 
Positive:  COUPTF2, DLX2, PROX1, GAD1, CXCR4, LHX6, LRP8, TSHZ1, CXCL14, EOMES 
       NKX2.1, SP8, CALB2, CXCL12, DCDC2, VLDLR 
Negative:  SATB2, RELN, MAF1, PAX6, ASCL1, SCGN, SST, EMX1, GSX2, NCAM1 
       DCX, KIA0319, VIP, EGFR, CXCR7, TBR1 
PC_ 4 
Positive:  NCAM1, TSHZ1, VLDLR, CXCL14, PROX1, EGFR, CXCR7, DCX, ASCL1, DCDC2 
       CALB2, PAX6, GSX2, SCGN, EOMES, KIA0319 
Negative:  LHX6, DLX2, LRP8, SP8, VIP, SST, COUPTF2, NKX2.1, TBR1, CXCR4 
       EMX1, RELN, CXCL12, MAF1, GAD1, SATB2 
PC_ 5 
Positive:  GSX2, SP8, NKX2.1, SCGN, COUPTF2, CXCL14, EGFR, EMX1, TSHZ1, CALB2 
       CXCL12, TBR1, PAX6, SATB2, MAF1, KIA0319 
Negative:  SST, CXCR4, DCDC2, GAD1, PROX1, EOMES, DLX2, VIP, DCX, VLDLR 
       RELN, NCAM1, LHX6, ASCL1, CXCR7, LRP8 

jy_408 <- FindNeighbors(jy_408, dims = 1:30)

Computing nearest neighbor graph
Computing SNN

jy_408 <- FindClusters(jy_408, resolution = 1.5)

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1013
Number of edges: 35954

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5629
Number of communities: 12
Elapsed time: 0 seconds

jy_408 <- RunUMAP(jy_408, dims = 1:30)

Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
17:52:20 UMAP embedding parameters a = 0.9922 b = 1.112
17:52:20 Read 1013 rows and found 30 numeric columns
17:52:20 Using Annoy for neighbor search, n_neighbors = 30
17:52:20 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:52:20 Writing NN index file to temp file /tmp/RtmpKuWa3v/filebb88168a050d
17:52:20 Searching Annoy index using 1 thread, search_k = 3000
17:52:20 Annoy recall = 100%
17:52:21 Commencing smooth kNN distance calibration using 1 thread
17:52:21 Initializing from normalized Laplacian + noise
17:52:21 Commencing optimization for 500 epochs, with 38030 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:52:22 Optimization finished

DimPlot(jy_408,  reduction = "umap", group.by = 'seurat_clusters') + NoAxes()

hcoords = df_408 %>% dplyr::select(c('X_horz', 'Y_horz')) %>% as.matrix()
colnames(hcoords) <- c('pixel_1', 'pixel_2')

jy_408[["H"]] <- CreateDimReducObject(embeddings = hcoords, key = "pixel_", assay = DefaultAssay(jy_408))

Merge both datasets and generate a metadata column that corresponds

to the cell

df_164 = data.frame()
for (file_name in list.files(data_dir)){
  print(file_name)
  if(grepl('408', file_name)){
    next
  }
  #if(grepl('408_TC', file_name) | grepl('408_vMS', file_name)){
  #  next
  #}
  df_to_append <- read.table(file.path(data_dir, file_name), sep = ',', header = TRUE)
  while(length(ind <- which(df_to_append$Image.Name == "")) > 0){
    df_to_append$Image.Name[ind] <- df_to_append$Image.Name[ind -1]
  }
  
  colnames(df_to_append) <- toupper(colnames(df_to_append))
  df_to_append <- df_to_append %>%
    mutate(area = strsplit(file_name, '.csv')[[1]])
  
  ## Add relative_XY_position
  
  if(!is_empty(df_164)){
    df_to_append <- df_to_append %>%
          dplyr::select(colnames(df_164))
  }
  df_164 <- rbind(df_164, df_to_append)
}

[1] "164_CC.csv"
[1] "164_MS_CC.csv"
[1] "164_MS_TC.csv"
[1] "164_TC.csv"
[1] "408_CC.csv"
[1] "408_dMS_TC.csv"
[1] "408_MS_CC.csv"
[1] "408_TC.csv"
[1] "408_vMS_TC.csv"

df_164$IMAGE.NAME = unlist(lapply(df_164$IMAGE.NAME, gsub, pattern='CC-', replacement='CC_'))
df_164$IMAGE.NAME = unlist(lapply(df_164$IMAGE.NAME, gsub, pattern='[*]', replacement=''))
df_164$IMAGE.NAME = unlist(lapply(df_164$IMAGE.NAME, gsub, pattern='X', replacement=''))
df_164$IMAGE.NAME = unlist(lapply(df_164$IMAGE.NAME, gsub, pattern='L2', replacement='CC_L2'))
df_164$IMAGE.NAME = unlist(lapply(df_164$IMAGE.NAME, gsub, pattern='L2_', replacement='L2-'))
df_164$IMAGE.NAME = unlist(lapply(df_164$IMAGE.NAME, gsub, pattern='-L2', replacement='_L2'))
tc_cortical_names_bad = df_164[grepl('TC', df_164$area) & grepl('Cortical', df_164$IMAGE.NAME), 'IMAGE.NAME']
df_164[grepl('TC', df_164$area) & grepl('Cortical', df_164$IMAGE.NAME), 'IMAGE.NAME'] = unlist(lapply(tc_cortical_names_bad, gsub, pattern='Cort', replacement='TC_Cort'))
cc_cortical_names_bad = df_164[grepl('CC', df_164$area) & grepl('Cortical', df_164$IMAGE.NAME), 'IMAGE.NAME']
df_164[grepl('CC', df_164$area) & grepl('Cortical', df_164$IMAGE.NAME), 'IMAGE.NAME'] = unlist(lapply(cc_cortical_names_bad, gsub, pattern='Cort', replacement='CC_Cort'))
#df_164$IMAGE.NAME = unlist(lapply(df_164$IMAGE.NAME, gsub, pattern='Tc_12', replacement='TC_12'))
## Missing
#df_164 = df_164[df_164$IMAGE.NAME != 'Layer1', ]
#df_164 = df_164[df_164$IMAGE.NAME != 'TC_1', ]
#df_164 = df_164[df_164$IMAGE.NAME != 'TC_18', ]
#df_164 = df_164[df_164$IMAGE.NAME != 'TC_19', ]
#df_164$IMAGE.NAME = toupper(df_164$IMAGE.NAME)
unique(df_164$IMAGE.NAME)

 [1] "CC_8"         "CC_10"        "CC_Cortical1" "CC_Cortical2" "CC_L2-1"      "CC_L2-2"      "CC_L2-3"      "CC_2"         "CC_3"         "CC_4"        
[11] "CC_5"         "CC_6"         "CC_7"         "CC_9"         "TC_1"         "TC_2"         "TC_3"         "TC_4"         "TC_5"         "TC_6"        
[21] "TC_7"         "TC_8"         "TC_9"         "TC_10"        "TC_Cortical1" "TC_Cortical2" "TC_Cortical3"

Now we know that everything is equal to one another, we should load the variable

image_names = unique(df_164$IMAGE.NAME)
# Preset these variables to negative values so I can easily check if they were updated later
df_164$X = -1
df_164$Y = -1
# set some normalization variables
## This is the size of the image when the pixel values are taken from top left down
IMAGE_SIZE = 1024
## This is the size of an image in the global coordinate space
IMAGE_LEN = 32
TC_IMAGE_HEIGHT = 410
TC_IMAGE_WIDTH = 446
CC_IMAGE_HEIGHT= 422
CC_IMAGE_WIDTH = 214

# Load the dataframe with global and relative coordinates
img_cords = read.table(file.path(meta_dir, '164_pixel_coordinates.csv'), sep = ',', header = TRUE)

images = list.files(meta_dir)
for(image_name in image_names){
    if(grepl('408', image_name)){
      next
    }
    print(image_name)
    split_names = strsplit(image_name, '_')
    cortex = toupper(split_names[[1]][1])
    number = split_names[[1]][2]
    number_csv = paste0('_', number, '.csv')
    filename = images[grepl(cortex, images) & grepl(number_csv, images) & grepl('164', images)]
    coordinates = read.table(file.path(meta_dir, filename), sep = ',', header = TRUE)
    if(image_name == "CC_L2-1"){
      coordinates = coordinates[c(1:37, 39:nrow(coordinates)), ]
    }
    if(cortex == 'CC'){ 
      print(paste('cc', filename, image_name))
      ## So if CC, we add the coordinates for TC_1 to overall image coordinates
      x_adj = img_cords[img_cords$Name == 'TC_1', 'x'] + 
                img_cords[img_cords$Name == 'G_CC1_to_TC1', 'x']
      ## Start from bottom, add the height, subtract TC_1 height, and then global CC1 to TC1
      y_adj = TC_IMAGE_HEIGHT - img_cords[img_cords$Name == 'TC_1', 'y'] +
                img_cords[img_cords$Name == 'G_CC1_to_TC1', 'y'] + CC_IMAGE_HEIGHT
    }else{
      print(paste('tc', filename, image_name))
      x_adj = 0
      y_adj = TC_IMAGE_HEIGHT
    }
    
    ## So don't do repelled for now
    #x_repelled <- (512 - coordinates$X_Coordinate_In_pixels)
    
    ## so the resized x distance is from left, so just add to the box location and adj
    df_164[df_164$IMAGE.NAME == image_name, 'X'] = (coordinates$X_Coordinate_In_pixels / 
                                                      IMAGE_SIZE * IMAGE_LEN) + 
                                                    img_cords[img_cords$Name == image_name, 'x'] + x_adj
    ## resized y distance
    df_164[df_164$IMAGE.NAME == image_name, 'Y'] = y_adj - img_cords[img_cords$Name == image_name, 'y'] - 
                                                      (coordinates$Y_Coordinate_In_pixels / IMAGE_SIZE * 
                                                      IMAGE_LEN)  
}

[1] "CC_8"
[1] "cc 164_CC_ROI_CC_8.csv CC_8"
[1] "CC_10"
[1] "cc 164_CC_ROI_CC_10.csv CC_10"
[1] "CC_Cortical1"
[1] "cc 164_CC_ROI_CC_Cortical1.csv CC_Cortical1"
[1] "CC_Cortical2"
[1] "cc 164_CC_ROI_CC_Cortical2.csv CC_Cortical2"
[1] "CC_L2-1"
[1] "cc 164_CC_ROI_CC_L2-1.csv CC_L2-1"
[1] "CC_L2-2"
[1] "cc 164_CC_ROI_CC_L2-2.csv CC_L2-2"
[1] "CC_L2-3"
[1] "cc 164_CC_ROI_CC_L2-3.csv CC_L2-3"
[1] "CC_2"
[1] "cc 164_CC_ROI_CC_2.csv CC_2"
[1] "CC_3"
[1] "cc 164_CC_ROI_CC_3.csv CC_3"
[1] "CC_4"
[1] "cc 164_CC_ROI_CC_4.csv CC_4"
[1] "CC_5"
[1] "cc 164_CC_ROI_CC_5.csv CC_5"
[1] "CC_6"
[1] "cc 164_CC_ROI_CC_6.csv CC_6"
[1] "CC_7"
[1] "cc 164_CC_ROI_CC_7.csv CC_7"
[1] "CC_9"
[1] "cc 164_CC_ROI_CC_9.csv CC_9"
[1] "TC_1"
[1] "tc 164_TC_ROI_TC_1.csv TC_1"
[1] "TC_2"
[1] "tc 164_TC_ROI_TC_2.csv TC_2"
[1] "TC_3"
[1] "tc 164_TC_ROI_TC_3.csv TC_3"
[1] "TC_4"
[1] "tc 164_TC_ROI_TC_4.csv TC_4"
[1] "TC_5"
[1] "tc 164_TC_ROI_TC_5.csv TC_5"
[1] "TC_6"
[1] "tc 164_TC_ROI_TC_6.csv TC_6"
[1] "TC_7"
[1] "tc 164_TC_ROI_TC_7.csv TC_7"
[1] "TC_8"
[1] "tc 164_TC_ROI_TC_8.csv TC_8"
[1] "TC_9"
[1] "tc 164_TC_ROI_TC_9.csv TC_9"
[1] "TC_10"
[1] "tc 164_TC_ROI_TC_10.csv TC_10"
[1] "TC_Cortical1"
[1] "tc 164_TC_ROI_TC_Cortical1.csv TC_Cortical1"
[1] "TC_Cortical2"
[1] "tc 164_TC_ROI_TC_Cortical2.csv TC_Cortical2"
[1] "TC_Cortical3"
[1] "tc 164_TC_ROI_TC_Cortical3.csv TC_Cortical3"

We have the coordinates for 408_TC and others

rownames(df_164) = 1:nrow(df_164)
jy_164 = df_164 %>%
  dplyr::select(-c(area, IMAGE.NAME, X, Y)) %>%
  t() %>%
  CreateSeuratObject()

just set everything from below 1 in ratio to zero

jy_164 <- NormalizeData(jy_164, scale.factor = 1e5) ###

Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

normed = GetAssayData(jy_164, slot = 'data')
normed[normed < 3] = 0
jy_164 <- SetAssayData(jy_164, slot = 'data', normed)

jy_164 <- FindVariableFeatures(jy_164, selection.method = "vst")

Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

all.genes <- rownames(jy_164)
jy_164 <- ScaleData(jy_164, features = all.genes)

Centering and scaling data matrix

  |                                                                                                                                                            
  |                                                                                                                                                      |   0%
  |                                                                                                                                                            
  |======================================================================================================================================================| 100%

jy_164 <- RunPCA(jy_164, approx = FALSE)

Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
PC_ 1 
Positive:  NKX2.1, MAF1, SCGN, PROX1, GAD1, SP8, VIP, LHX6, GSX2, DCX 
       TSHZ1, CXCR7, COUPTF2, SST, DLX2, LRP8 
Negative:  KIA0319, SATB2, ASCL1, PAX6, CALB2, DCDC2, RELN, NCAM1, CXCL12, TBR1 
       EMX1, EGFR, CXCL14, VLDLR, CXCR4, EOMES 
PC_ 2 
Positive:  DCX, SCGN, SP8, TBR1, EGFR, SATB2, DCDC2, EOMES, NKX2.1, LRP8 
       KIA0319, NCAM1, EMX1, CXCR7, TSHZ1, CALB2 
Negative:  GAD1, VIP, CXCR4, LHX6, MAF1, DLX2, SST, RELN, CXCL12, CXCL14 
       COUPTF2, PROX1, PAX6, GSX2, ASCL1, VLDLR 
PC_ 3 
Positive:  COUPTF2, SP8, PROX1, SCGN, EOMES, TBR1, MAF1, CXCR7, NKX2.1, GSX2 
       TSHZ1, LHX6, DCDC2, EGFR, VIP, LRP8 
Negative:  SST, ASCL1, PAX6, RELN, CALB2, CXCL14, EMX1, CXCL12, DLX2, NCAM1 
       GAD1, CXCR4, KIA0319, DCX, VLDLR, SATB2 
PC_ 4 
Positive:  TSHZ1, PROX1, SP8, ASCL1, DLX2, VLDLR, NKX2.1, NCAM1, PAX6, CXCR7 
       SCGN, EMX1, RELN, CXCL14, VIP, KIA0319 
Negative:  LRP8, TBR1, EOMES, CALB2, LHX6, GSX2, COUPTF2, DCX, MAF1, GAD1 
       CXCL12, DCDC2, SATB2, EGFR, CXCR4, SST 
PC_ 5 
Positive:  PAX6, COUPTF2, RELN, TSHZ1, DLX2, SP8, CXCL12, SCGN, TBR1, GSX2 
       LRP8, DCX, SATB2, LHX6, ASCL1, GAD1 
Negative:  NKX2.1, DCDC2, EOMES, VLDLR, NCAM1, SST, CXCR7, EMX1, CXCR4, EGFR 
       MAF1, KIA0319, VIP, PROX1, CXCL14, CALB2 

jy_164 <- FindNeighbors(jy_164, dims = 1:30)

Computing nearest neighbor graph
Computing SNN

jy_164 <- FindClusters(jy_164, resolution = 0.8)

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 802
Number of edges: 30100

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6519
Number of communities: 6
Elapsed time: 0 seconds

jy_164 <- RunUMAP(jy_164, dims = 1:30)

17:52:24 UMAP embedding parameters a = 0.9922 b = 1.112
17:52:24 Read 802 rows and found 30 numeric columns
17:52:24 Using Annoy for neighbor search, n_neighbors = 30
17:52:24 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:52:25 Writing NN index file to temp file /tmp/RtmpKuWa3v/filebb88138feb5f2
17:52:25 Searching Annoy index using 1 thread, search_k = 3000
17:52:25 Annoy recall = 100%
17:52:25 Commencing smooth kNN distance calibration using 1 thread
17:52:25 Initializing from normalized Laplacian + noise
17:52:25 Commencing optimization for 500 epochs, with 30056 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:52:26 Optimization finished

DimPlot(jy_164,  reduction = "umap", group.by = 'seurat_clusters') + NoAxes()

unique(df_164$IMAGE.NAME)

 [1] "CC_8"         "CC_10"        "CC_Cortical1" "CC_Cortical2" "CC_L2-1"      "CC_L2-2"      "CC_L2-3"      "CC_2"         "CC_3"         "CC_4"        
[11] "CC_5"         "CC_6"         "CC_7"         "CC_9"         "TC_1"         "TC_2"         "TC_3"         "TC_4"         "TC_5"         "TC_6"        
[21] "TC_7"         "TC_8"         "TC_9"         "TC_10"        "TC_Cortical1" "TC_Cortical2" "TC_Cortical3"

images_ordered = c('TC_Cortical3', 'TC_Cortical2', 'TC_Cortical1', 'TC_10', 'TC_9', 'TC_8', 'TC_7', 'TC_6', 'TC_5', 'TC_4', 'TC_3', 'TC_2','TC_1','CC_2','CC_3',
           'CC_4', 'CC_5', 'CC_6', 'CC_7', 'CC_8', 'CC_9', 'CC_10',
           'CC_L2-1', 'CC_L2-2', 'CC_L2-3', 'CC_Cortical1', 'CC_Cortical2')

x_horz = 1:length(images_ordered) * 35
y_horz = rep(0, length(images_ordered))
horz_embedding = data.frame()
df_164$X_horz = -1
df_164$Y_horz = -1

images = list.files(meta_dir)
for(i in 1:length(images_ordered)){
    image_name = images_ordered[i]
    print(image_name)
    split_names = strsplit(image_name, '_')
    cortex = toupper(split_names[[1]][1])
    number = split_names[[1]][2]
    number_csv = paste0('_', number, '.csv')
    filename = images[grepl(cortex, images) & grepl(number_csv, images) & grepl('164', images)]
    coordinates = read.table(file.path(meta_dir, filename), sep = ',', header = TRUE)
    if(image_name == "CC_L2-1"){
      coordinates = coordinates[c(1:37, 39:nrow(coordinates)), ]
    }
    ## checked already that lists are equal, missing 1, 18, 19 for now, layer 1 and others
 
    ## so this is a little tricky, so need to get it right
    ## Remember, it is the top right that the coordinate is coming from, but
    ## the bottom right is the new coordinate space.
    ## so first when we get the original coordinate space, to set to relative
    ## of bottom would be the same X, but 1024 - Y
    
    ## push out the coordinates for better visualization
    #x_repelled <- (512 - coordinates$X_Coordinate_In_pixels)
    
    
    df_164[df_164$IMAGE.NAME == image_name, 'X_horz'] = (coordinates$X_Coordinate_In_pixels / 
                                                      IMAGE_SIZE * IMAGE_LEN) + y_horz[i]
    df_164[df_164$IMAGE.NAME == image_name, 'Y_horz'] = ((1024-coordinates$Y_Coordinate_In_pixels) / 
                                                      IMAGE_SIZE * IMAGE_LEN) + x_horz[i]
}

[1] "TC_Cortical3"
[1] "TC_Cortical2"
[1] "TC_Cortical1"
[1] "TC_10"
[1] "TC_9"
[1] "TC_8"
[1] "TC_7"
[1] "TC_6"
[1] "TC_5"
[1] "TC_4"
[1] "TC_3"
[1] "TC_2"
[1] "TC_1"
[1] "CC_2"
[1] "CC_3"
[1] "CC_4"
[1] "CC_5"
[1] "CC_6"
[1] "CC_7"
[1] "CC_8"
[1] "CC_9"
[1] "CC_10"
[1] "CC_L2-1"
[1] "CC_L2-2"
[1] "CC_L2-3"
[1] "CC_Cortical1"
[1] "CC_Cortical2"

hcoords = df_164 %>% dplyr::select(c('X_horz', 'Y_horz')) %>% as.matrix()
colnames(hcoords) <- c('pixel_1', 'pixel_2')

jy_164[["H"]] <- CreateDimReducObject(embeddings = hcoords, key = "pixel_", assay = DefaultAssay(jy_164))

jy_164<- RenameCells(jy_164, c(outer('164_', 1:ncol(jy_164), FUN=paste0)))
jy_164$area = df_164$area
jy_408<- RenameCells(jy_408, c(outer('408_', 1:ncol(jy_408), FUN=paste0)))
jy_408$area = df_408$area
jy_all <- merge(jy_164, jy_408)

jy_all <- NormalizeData(jy_all, scale.factor = 1e5) ###

Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

normed = GetAssayData(jy_all, slot = 'data')
normed[normed < 3] = 0
jy_all <- SetAssayData(jy_all, slot = 'data', normed)

jy_all <- FindVariableFeatures(jy_all, selection.method = "vst")

Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

all.genes <- rownames(jy_all)
jy_all <- ScaleData(jy_all, features = all.genes)

Centering and scaling data matrix

  |                                                                                                                                                            
  |                                                                                                                                                      |   0%
  |                                                                                                                                                            
  |======================================================================================================================================================| 100%

jy_all <- RunPCA(jy_all, approx = FALSE)

Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
Warning: Requested number is larger than the number of available items (32). Setting to 32.
PC_ 1 
Positive:  ASCL1, CXCR4, KIA0319, SATB2, RELN, PAX6, CXCL12, EMX1, VIP, CALB2 
       DCDC2, DLX2, VLDLR, EOMES, SST, LHX6 
Negative:  DCX, SCGN, GSX2, NKX2.1, TSHZ1, TBR1, LRP8, COUPTF2, SP8, EGFR 
       CXCR7, CXCL14, PROX1, MAF1, GAD1, NCAM1 
PC_ 2 
Positive:  GAD1, MAF1, VIP, LHX6, NKX2.1, PROX1, DLX2, CXCR4, SST, TSHZ1 
       SP8, GSX2, VLDLR, RELN, CXCR7, COUPTF2 
Negative:  TBR1, DCX, KIA0319, DCDC2, LRP8, EOMES, SATB2, EGFR, CALB2, CXCL12 
       NCAM1, EMX1, PAX6, ASCL1, CXCL14, SCGN 
PC_ 3 
Positive:  NCAM1, RELN, ASCL1, PAX6, SATB2, SST, MAF1, EMX1, VLDLR, EGFR 
       CXCR7, CXCL14, TSHZ1, DCX, SCGN, GSX2 
Negative:  COUPTF2, LRP8, LHX6, EOMES, TBR1, SP8, GAD1, DLX2, CXCR4, PROX1 
       NKX2.1, CALB2, CXCL12, DCDC2, VIP, KIA0319 
PC_ 4 
Positive:  SST, RELN, DLX2, LRP8, LHX6, PAX6, GAD1, CALB2, CXCL12, CXCR4 
       TBR1, VIP, ASCL1, SATB2, KIA0319, EMX1 
Negative:  TSHZ1, PROX1, CXCR7, NCAM1, SCGN, NKX2.1, EGFR, VLDLR, SP8, CXCL14 
       GSX2, DCX, DCDC2, COUPTF2, EOMES, MAF1 
PC_ 5 
Positive:  SP8, SCGN, PAX6, DLX2, EMX1, NKX2.1, SATB2, COUPTF2, ASCL1, SST 
       RELN, PROX1, VLDLR, TBR1, DCX, KIA0319 
Negative:  GAD1, CXCL14, NCAM1, EGFR, VIP, LRP8, DCDC2, CXCR4, MAF1, CXCR7 
       GSX2, LHX6, CXCL12, EOMES, CALB2, TSHZ1 

jy_all <- FindNeighbors(jy_all, dims = 1:30)

Computing nearest neighbor graph
Computing SNN

jy_all <- FindClusters(jy_all, resolution = 1.5)

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1815
Number of edges: 61694

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6181
Number of communities: 13
Elapsed time: 0 seconds

jy_all <- RunUMAP(jy_all, dims = 1:30)

17:52:28 UMAP embedding parameters a = 0.9922 b = 1.112
17:52:28 Read 1815 rows and found 30 numeric columns
17:52:28 Using Annoy for neighbor search, n_neighbors = 30
17:52:28 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:52:28 Writing NN index file to temp file /tmp/RtmpKuWa3v/filebb88165be5c09
17:52:28 Searching Annoy index using 1 thread, search_k = 3000
17:52:29 Annoy recall = 100%
17:52:29 Commencing smooth kNN distance calibration using 1 thread
17:52:30 Initializing from normalized Laplacian + noise
17:52:30 Commencing optimization for 500 epochs, with 70074 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:52:32 Optimization finished

DimPlot(jy_all,  reduction = "umap", group.by = 'seurat_clusters') + NoAxes()

big_dimplot <- function(sobj, grep_pattern){
  dp = DimPlot(sobj, cells.highlight = list(imp = which(grepl(grep_pattern, sobj$area))))
  dp <- dp + scale_color_manual(values = c('grey90', '#1982c4'), labels=c('other', grep_pattern)) + NoAxes()
}
patterns = c('408_CC', '408_MS_CC', 'vMS_TC', 'dMS_TC', '408_TC', '164_CC', '164_MS_CC', '164_MS_TC',  '164_TC')
plots <- lapply(1:length(patterns), function(i){
    big_dimplot(jy_all, grep_pattern = patterns[i])
  })

Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.

areas = plot_grid(plotlist = plots, label_size = 10, nrow = 3)
areas

ggsave(plot = areas, filename = 'test_all_area_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 14, height = 8, dpi = 150)

plot_clusters_umap(jy_all, clustering ='RNA_snn_res.1.5', pt.size = 2.0)

Error in plot_clusters_umap(jy_all, clustering = "RNA_snn_res.1.5", pt.size = 2) : 
  could not find function "plot_clusters_umap"

jy_all.markers <- FindAllMarkers(jy_all, only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25)

Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

jy_all.markers %>%
   group_by(cluster) %>%
   slice_max(n = 32, order_by = avg_log2FC)

clusters_164 = jy_all$RNA_snn_res.1.5[1:ncol(jy_164)]
jy_164$unified_clusters = clusters_164
clusters_408 = jy_all$RNA_snn_res.1.5[(ncol(jy_164)+1):ncol(jy_all)]
jy_408$unified_clusters = clusters_408

clusters = as.numeric(sort(unique(jy_408$unified_clusters)))
plots <- lapply(1:length(clusters), function(i){
    plot_clusters_vertical_spatial(jy_408, cluster = clusters[i], pt.size = 1, clustering = 'unified_clusters', anterior = FALSE)
  })
verts= plot_grid(plotlist = plots, label_size = 10, nrow = 1)
ggsave(plot = verts, filename = 'test_408_unified_vertical_cluster_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 5, height = 8, dpi = 150)

clusters = as.numeric(sort(unique(jy_164$unified_clusters)))
plots <- lapply(1:length(clusters), function(i){
    plot_clusters_vertical_spatial(jy_164, cluster = clusters[i], pt.size = 1, clustering = 'unified_clusters', anterior = TRUE)
  })
verts= plot_grid(plotlist = plots, label_size = 10, nrow = 1)
ggsave(plot = verts, filename = 'test_164_unified_vertical_cluster_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 5, height = 8, dpi = 150)

genes = rownames(markers2)
plots <- lapply(1:length(genes), function(i){
    plot_features_umap(jy_all, genes[i], pt.size = 0.5)
  })
umaps = plot_grid(plotlist = plots, label_size = 10, nrow = 1)
umaps
ggsave(plot = umaps, filename = 'cluster7_markers_all_umapl_expr_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 8, height = 1, dpi = 150)

jy_all_7.markers <- FindMarkers(jy_all, ident.1 = 7, ident.2 = NULL, only.pos = FALSE)
markers2 = jy_all_7.markers %>%
   slice_max(n = 5, order_by = avg_log2FC)
markers2

new.cluster.ids = c('TBR1+/LRP8+ MS to TC', 
              'PROX1 and NKX2.1 Immature INs',
'Immature CALB2+ CGE IN',
 'Excitatory CXCL12+ Neurons',
'GSX2- dLGE INs',
'Mature, SST+ MGE INs',
 'Mature, VIP+ CGE INs',
 'MAF1+/TSHZ1+ Immature INs',
 'Layer 2 Excitatory Neurons',
 'CXCR4+ Posterior, MS to TC INs',
'EMX1+/NKX2.1+ Anterior, MS to CC INs',
 'EMX1+/LHX6+ Posterior, MS to CC INs',
 'GSX2+/RELN+/PAX6+ dLGE INs')

names(new.cluster.ids) <- levels(jy_all)
jy_all <- RenameIdents(jy_all, new.cluster.ids)

library(ggrepel)
plot_clusters_umap <- function(sobj, clustering, pt.size = 3, space = "umap")
{
  coordinates <- Embeddings(sobj, reduction = space)
  #expmat <- sobj[[clustering]]
  expmat  = as.character(Idents(jy_all))
  gene_df <- as.data.frame(cbind(coordinates, expmat))
  colnames(gene_df) <- c('X', 'Y', 'expr')
  gene_df$X = as.numeric(gene_df$X)
  gene_df$Y = as.numeric(gene_df$Y)
  summary_gene_df = gene_df %>% dplyr::group_by(expr) %>% dplyr::summarise(xmean = mean(X), ymean = mean(Y))
  plot <- ggplot(gene_df, aes(x = X, y = Y, color = as.factor(expr))) + geom_point(size = pt.size, alpha = 0.8) + #+ geom_label_repel(data = summary_gene_df,
                                                                                                                # mapping = aes(x = xmean, 
                           #y = ymean), 
                           #label = summary_gene_df$expr) +
            theme_classic() + ggtitle(clustering) + NoAxes() + #NoLegend()  + 
    theme(title = element_text(face = 'bold', size = rel(1), hjust = 1)) 
  cluster_colors = scales::hue_pal()(length(unique(expmat)))
  plot = plot + scale_colour_manual(values = cluster_colors)
  return(plot)
}

plot_clusters_umap(jy_all, clustering = '', pt.size = 2.0)

immature_IN_names = c('PROX1 and NKX2.1 Immature INs',
'Immature CALB2+ CGE interneuron',
 'MAF1+/TSHZ1+ Immature INs',
 'CXCR4+ Posterior, MS to TC INs',
'EMX1+/NKX2.1+ Anterior, MS to CC INs',
 'EMX1+/LHX6+ Posterior, MS to CC INs',
 'GSX2+/RELN+/PAX6+ Clump')

jy_immature <- jy_all[, Idents(jy_all) %in% immature_IN_names]

breakpoints = 1:20/10+0.3
plots = list()
jy_immature <- FindNeighbors(jy_immature, dims = 1:30)

Computing nearest neighbor graph
Computing SNN

i = 1
for (breakpoint in breakpoints){
  jy_immature <- FindClusters(jy_immature, resolution = breakpoint)
  jy_immature <- RunUMAP(jy_immature, dims = 1:30)
  jy_immature.markers <- FindAllMarkers(jy_immature, only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25)
  labels = jy_immature.markers %>%
   group_by(cluster) %>%
   slice_max(n = 1, order_by = avg_log2FC)
  new.cluster.ids <- labels$gene
  names(new.cluster.ids) <- levels(jy_immature)
  jy_immature <- RenameIdents(jy_immature, new.cluster.ids)
  plots[[i]] = DimPlot(jy_immature, reduction = "umap", pt.size = 1, label = TRUE) + NoAxes() + NoLegend() + ggtitle(breakpoint)
  i = i + 1
}

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.7886
Number of communities: 5
Elapsed time: 0 seconds

00:33:01 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:01 Read 786 rows and found 30 numeric columns
00:33:01 Using Annoy for neighbor search, n_neighbors = 30
00:33:01 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:01 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f044020edf1
00:33:01 Searching Annoy index using 1 thread, search_k = 3000
00:33:01 Annoy recall = 100%
00:33:01 Commencing smooth kNN distance calibration using 1 thread
00:33:02 Initializing from normalized Laplacian + noise
00:33:02 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:03 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |+++++++                                           | 13% ~00s          
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++                          | 47% ~00s          
  |+++++++++++++++++++++++++++                       | 53% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 87% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.7560
Number of communities: 6
Elapsed time: 0 seconds

00:33:03 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:03 Read 786 rows and found 30 numeric columns
00:33:03 Using Annoy for neighbor search, n_neighbors = 30
00:33:03 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:04 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0427cd431a
00:33:04 Searching Annoy index using 1 thread, search_k = 3000
00:33:04 Annoy recall = 100%
00:33:04 Commencing smooth kNN distance calibration using 1 thread
00:33:05 Initializing from normalized Laplacian + noise
00:33:05 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:06 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.7291
Number of communities: 6
Elapsed time: 0 seconds

00:33:06 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:06 Read 786 rows and found 30 numeric columns
00:33:06 Using Annoy for neighbor search, n_neighbors = 30
00:33:06 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:06 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f045dbf24c
00:33:06 Searching Annoy index using 1 thread, search_k = 3000
00:33:07 Annoy recall = 100%
00:33:07 Commencing smooth kNN distance calibration using 1 thread
00:33:08 Initializing from normalized Laplacian + noise
00:33:08 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:09 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.7022
Number of communities: 6
Elapsed time: 0 seconds

00:33:09 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:09 Read 786 rows and found 30 numeric columns
00:33:09 Using Annoy for neighbor search, n_neighbors = 30
00:33:09 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:09 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f043bd0dbd8
00:33:09 Searching Annoy index using 1 thread, search_k = 3000
00:33:09 Annoy recall = 100%
00:33:10 Commencing smooth kNN distance calibration using 1 thread
00:33:10 Initializing from normalized Laplacian + noise
00:33:10 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:12 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6773
Number of communities: 6
Elapsed time: 0 seconds

00:33:12 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:12 Read 786 rows and found 30 numeric columns
00:33:12 Using Annoy for neighbor search, n_neighbors = 30
00:33:12 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:12 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f046b090e3b
00:33:12 Searching Annoy index using 1 thread, search_k = 3000
00:33:12 Annoy recall = 100%
00:33:13 Commencing smooth kNN distance calibration using 1 thread
00:33:13 Initializing from normalized Laplacian + noise
00:33:13 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:14 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6532
Number of communities: 6
Elapsed time: 0 seconds

00:33:15 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:15 Read 786 rows and found 30 numeric columns
00:33:15 Using Annoy for neighbor search, n_neighbors = 30
00:33:15 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:15 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f042c056235
00:33:15 Searching Annoy index using 1 thread, search_k = 3000
00:33:15 Annoy recall = 100%
00:33:16 Commencing smooth kNN distance calibration using 1 thread
00:33:16 Initializing from normalized Laplacian + noise
00:33:16 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:17 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6298
Number of communities: 7
Elapsed time: 0 seconds

00:33:18 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:18 Read 786 rows and found 30 numeric columns
00:33:18 Using Annoy for neighbor search, n_neighbors = 30
00:33:18 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:18 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0447441d4f
00:33:18 Searching Annoy index using 1 thread, search_k = 3000
00:33:18 Annoy recall = 100%
00:33:18 Commencing smooth kNN distance calibration using 1 thread
00:33:19 Initializing from normalized Laplacian + noise
00:33:19 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:20 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6063
Number of communities: 7
Elapsed time: 0 seconds

00:33:21 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:21 Read 786 rows and found 30 numeric columns
00:33:21 Using Annoy for neighbor search, n_neighbors = 30
00:33:21 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:21 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0433a47f83
00:33:21 Searching Annoy index using 1 thread, search_k = 3000
00:33:21 Annoy recall = 100%
00:33:21 Commencing smooth kNN distance calibration using 1 thread
00:33:22 Initializing from normalized Laplacian + noise
00:33:22 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:23 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5897
Number of communities: 9
Elapsed time: 0 seconds

00:33:24 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:24 Read 786 rows and found 30 numeric columns
00:33:24 Using Annoy for neighbor search, n_neighbors = 30
00:33:24 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:24 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f04154a3cea
00:33:24 Searching Annoy index using 1 thread, search_k = 3000
00:33:24 Annoy recall = 100%
00:33:24 Commencing smooth kNN distance calibration using 1 thread
00:33:25 Initializing from normalized Laplacian + noise
00:33:25 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:26 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5764
Number of communities: 9
Elapsed time: 0 seconds

00:33:27 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:27 Read 786 rows and found 30 numeric columns
00:33:27 Using Annoy for neighbor search, n_neighbors = 30
00:33:27 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:27 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f045571094e
00:33:27 Searching Annoy index using 1 thread, search_k = 3000
00:33:27 Annoy recall = 100%
00:33:27 Commencing smooth kNN distance calibration using 1 thread
00:33:28 Initializing from normalized Laplacian + noise
00:33:28 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:29 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5635
Number of communities: 10
Elapsed time: 0 seconds

00:33:30 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:30 Read 786 rows and found 30 numeric columns
00:33:30 Using Annoy for neighbor search, n_neighbors = 30
00:33:30 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:30 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f046209aee5
00:33:30 Searching Annoy index using 1 thread, search_k = 3000
00:33:30 Annoy recall = 100%
00:33:30 Commencing smooth kNN distance calibration using 1 thread
00:33:31 Initializing from normalized Laplacian + noise
00:33:31 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:32 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5507
Number of communities: 10
Elapsed time: 0 seconds

00:33:33 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:33 Read 786 rows and found 30 numeric columns
00:33:33 Using Annoy for neighbor search, n_neighbors = 30
00:33:33 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:33 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f04418e8957
00:33:33 Searching Annoy index using 1 thread, search_k = 3000
00:33:33 Annoy recall = 100%
00:33:33 Commencing smooth kNN distance calibration using 1 thread
00:33:34 Initializing from normalized Laplacian + noise
00:33:34 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:35 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5380
Number of communities: 10
Elapsed time: 0 seconds

00:33:36 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:36 Read 786 rows and found 30 numeric columns
00:33:36 Using Annoy for neighbor search, n_neighbors = 30
00:33:36 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:36 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0424306e45
00:33:36 Searching Annoy index using 1 thread, search_k = 3000
00:33:36 Annoy recall = 100%
00:33:36 Commencing smooth kNN distance calibration using 1 thread
00:33:37 Initializing from normalized Laplacian + noise
00:33:37 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:38 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5250
Number of communities: 11
Elapsed time: 0 seconds

00:33:39 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:39 Read 786 rows and found 30 numeric columns
00:33:39 Using Annoy for neighbor search, n_neighbors = 30
00:33:39 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:39 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0427a7e0aa
00:33:39 Searching Annoy index using 1 thread, search_k = 3000
00:33:39 Annoy recall = 100%
00:33:39 Commencing smooth kNN distance calibration using 1 thread
00:33:40 Initializing from normalized Laplacian + noise
00:33:40 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:41 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5139
Number of communities: 11
Elapsed time: 0 seconds

00:33:42 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:42 Read 786 rows and found 30 numeric columns
00:33:42 Using Annoy for neighbor search, n_neighbors = 30
00:33:42 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:42 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0428ceba0c
00:33:42 Searching Annoy index using 1 thread, search_k = 3000
00:33:42 Annoy recall = 100%
00:33:43 Commencing smooth kNN distance calibration using 1 thread
00:33:43 Initializing from normalized Laplacian + noise
00:33:43 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:44 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5031
Number of communities: 11
Elapsed time: 0 seconds

00:33:45 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:45 Read 786 rows and found 30 numeric columns
00:33:45 Using Annoy for neighbor search, n_neighbors = 30
00:33:45 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:45 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f044337e03d
00:33:45 Searching Annoy index using 1 thread, search_k = 3000
00:33:45 Annoy recall = 100%
00:33:46 Commencing smooth kNN distance calibration using 1 thread
00:33:46 Initializing from normalized Laplacian + noise
00:33:46 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:47 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.4922
Number of communities: 11
Elapsed time: 0 seconds

00:33:48 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:48 Read 786 rows and found 30 numeric columns
00:33:48 Using Annoy for neighbor search, n_neighbors = 30
00:33:48 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:48 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f044b2835a6
00:33:48 Searching Annoy index using 1 thread, search_k = 3000
00:33:48 Annoy recall = 100%
00:33:49 Commencing smooth kNN distance calibration using 1 thread
00:33:49 Initializing from normalized Laplacian + noise
00:33:49 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:50 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.4812
Number of communities: 12
Elapsed time: 0 seconds

1 singletons identified. 11 final clusters.
00:33:51 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:51 Read 786 rows and found 30 numeric columns
00:33:51 Using Annoy for neighbor search, n_neighbors = 30
00:33:51 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:51 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0457c42863
00:33:51 Searching Annoy index using 1 thread, search_k = 3000
00:33:51 Annoy recall = 100%
00:33:52 Commencing smooth kNN distance calibration using 1 thread
00:33:52 Initializing from normalized Laplacian + noise
00:33:53 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:54 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.4704
Number of communities: 13
Elapsed time: 0 seconds

1 singletons identified. 12 final clusters.
00:33:54 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:54 Read 786 rows and found 30 numeric columns
00:33:54 Using Annoy for neighbor search, n_neighbors = 30
00:33:54 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:54 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0447bc00b8
00:33:54 Searching Annoy index using 1 thread, search_k = 3000
00:33:55 Annoy recall = 100%
00:33:55 Commencing smooth kNN distance calibration using 1 thread
00:33:56 Initializing from normalized Laplacian + noise
00:33:56 Commencing optimization for 500 epochs, with 29334 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:57 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

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Calculating cluster 8

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Calculating cluster 9

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Calculating cluster 10

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Calculating cluster 11

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Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 786
Number of edges: 29724

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.4600
Number of communities: 12
Elapsed time: 0 seconds

00:33:57 UMAP embedding parameters a = 0.9922 b = 1.112
00:33:57 Read 786 rows and found 30 numeric columns
00:33:57 Using Annoy for neighbor search, n_neighbors = 30
00:33:57 Building Annoy index with metric = cosine, n_trees = 50
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:33:58 Writing NN index file to temp file /tmp/RtmpIqRk2o/file74f0435b8e4be
00:33:58 Searching Annoy index using 1 thread, search_k = 3000
00:33:58 Annoy recall = 100%
00:33:58 Commencing smooth kNN distance calibration using 1 thread
00:33:59 Initializing from normalized Laplacian + noise
00:33:59 Commencing optimization for 500 epochs, with 29334 positive edges
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:34:00 Optimization finished
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Calculating cluster 1

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Calculating cluster 3

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Calculating cluster 6

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Calculating cluster 7

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Calculating cluster 8

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Calculating cluster 9

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Calculating cluster 10

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Calculating cluster 11

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marrangeGrob(plots, nrow=2, ncol=2)

ml <- marrangeGrob(plots, nrow=2, ncol=2)
ggsave(filename = 'immature_sequential_clustering_umaps.pdf', path = file.path(output_dir_plot, '20220721_1'), ml)

Saving 7.29 x 4.5 in image

make an easy mapping

get_broad_type <- function(celltype){
  Excitatory =  c('Layer 2 Excitatory Neurons',
                  'Excitatory CXCL12+ Neurons',
                  'Cajal Retzius Cells',
                  'Immature CALB2+ CGE interneuron')
  Mature_inhib = c('Mature, SST+ MGE INs',
                   "Mature, VIP+ CGE INs")
  other = c('TBR1+/LRP8+ MS to TC')
    
  immature_neurons = c(
  'PROX1 and NKX2.1 Immature INs',
 'MAF1+/TSHZ1+ Immature INs',
 'CXCR4+ Posterior, MS to TC INs',
'EMX1+/NKX2.1+ Anterior, MS to CC INs',
 'EMX1+/LHX6+ Posterior, MS to CC INs',
 'GSX2+/RELN+/PAX6+ Clump')
  if(celltype %in% Excitatory){
    return("EN")
  }else if(celltype %in% Mature_inhib){
    return('Mature IN')
  } else if(celltype %in% immature_neurons){
    return('Immature IN')
  } else{return('other')} 
}

do heatmap real quick

# get the scaled data
scaled_values = as.matrix(GetAssayData(jy_all, slot = "data"))

genes_to_remove = c('DCX', 'DCDC2', 'KIA0319', 'NCAM1')

#cluster_ordering = sort(as.character(Idents(jy_all)), index.return = TRUE)
scaled_values = scaled_values[!rownames(scaled_values)%in% genes_to_remove,]

### Apply separate clustering, need to look into why 
hr <- hclust(as.dist(1-cor(t(scaled_values), method="pearson")), method = "complete")
#hc <- hclust(as.dist(1-cor(scaled_values, method="spearman")), method="complete")

broad_labels = unlist(lapply(1:ncol(scaled_values), function(i){
  get_broad_type(as.character(Idents(jy_all))[i])
}))
#broad_order = sort(broad_labels, index.return = TRUE)
#final_ox = order( cluster_ordering$x, broad_order$x)
#final_ox = broad_order$ix

#gaps = c()
#for(i in 2:length(broad_order$x)){
#  if(broad_order$x[i] != broad_order$x[i-1]){
#    gaps = c(gaps, i)
#    print(i)
#  }
#}

broad_area_sorted = sort(jy_all$area, index.return = TRUE)
final_ox = broad_area_sorted$ix

gaps = c()
for(i in 2:length(broad_area_sorted$x)){
  if(broad_area_sorted$x[i] != broad_area_sorted$x[i-1]){
    gaps = c(gaps, i)
    print(i)
  }
}

[1] 250
[1] 431
[1] 699
[1] 803
[1] 974
[1] 1282
[1] 1536
[1] 1626

### Now arrange everything

annotation <- data.frame(cell_type = as.character(Idents(jy_all)),
                         #cell_class = broad_labels,
                         area = jy_all$area)
rownames(annotation) <- colnames(scaled_values) # check out the row names of annotation

scaled_values[, final_ox] %>%
  pheatmap(annotation_col = annotation, 
           color = colorRampPalette(brewer.pal(n = 9, name = "Purples"))(100),
  #breaks = seq(from= -5, to = 5, by = 11/100.), 
  cluster_rows = hr, #cluster_cols = hc, 
  #cluster_rows = TRUE,
  cluster_cols = FALSE,
  #clustering_distance_rows = "correlation", 
  #clustering_distance_cols = "correlation",
  fontsize_row = 8, fontsize_col = 4, show_colnames = FALSE, gaps_col = gaps,
           show_rownames = TRUE, cell_width = 10, cellheight = 8, width = 10, height = 14)#,

          #  filename = file.path(file.path(output_dir_plot, '20220721_1'), 'ncol_20_sort_by_broad_type_gaps.png'))

plot_features_umap <- function(sobj, gene, pt.size = 3, alpha = 0.8, space = "umap", color = '#CB2A55', flipped = FALSE)
{
  coordinates <- Embeddings(sobj, reduction = space)
  expmat <- as.matrix(FetchData(sobj, gene))
  gene_df <- as.data.frame(cbind(coordinates, expmat))
  colnames(gene_df) <- c('X', 'Y', 'expr')
  gene_df <- gene_df %>% dplyr::arrange(!is.na(expr), expr)
  colors = c('grey90', 'grey90', color)
  gene_df$expr[gene_df$expr == 0] = NA
  plot <- ggplot(gene_df, aes(x = X, y = Y, color = expr)) + geom_point(size = pt.size, alpha = alpha)+  
            theme_classic() + ggtitle(gene) +  scale_color_gradient(na.value = colors[1], low = colors[2], high = colors[3], labels = NULL)  + theme(title = element_text(face = 'bold', size = rel(1), hjust = 1)) 
  if(flipped){
    plot <- plot + scale_x_reverse() + scale_y_reverse()
  }
  return(plot + NoAxes() + NoLegend())
}

genes = rownames(jy_immature)
plots <- lapply(1:length(genes), function(i){
    plot_features_umap(jy_immature, genes[i], pt.size = 0.5)
  })
umaps = plot_grid(plotlist = plots, label_size = 10, nrow = 4)
umaps

ggsave(plot = umaps, filename = 'test_immature_umapl_expr_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 10, height = 4, dpi = 150)

big_dimplot <- function(sobj, grep_pattern){
  dp = DimPlot(sobj, cells.highlight = list(imp = which(grepl(grep_pattern, sobj$area))))
  dp <- dp + scale_color_manual(values = c('grey90', '#1982c4'), labels=c('other', grep_pattern)) + NoAxes()
}
patterns = c('408_CC', '408_MS_CC', 'vMS_TC', 'dMS_TC', '408_TC', '164_CC', '164_MS_CC', '164_MS_TC',  '164_TC')
plots <- lapply(1:length(patterns), function(i){
    big_dimplot(jy_immature, grep_pattern = patterns[i])
  })

Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.

areas = plot_grid(plotlist = plots, label_size = 10, nrow = 3)
areas

ggsave(plot = areas, filename = 'test_immature_area_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 14, height = 8, dpi = 150)

jy_immature$seurat_clusters = jy_immature$RNA_snn_res.1.1
Idents(jy_immature) = jy_immature$seurat_clusters

DimPlot(jy_immature)

genes = rownames(markers2)
plots <- lapply(1:length(genes), function(i){
    plot_features_umap(jy_immature, genes[i], pt.size = 0.5)
  })
umaps = plot_grid(plotlist = plots, label_size = 10, nrow = 1)
umaps

ggsave(plot = umaps, filename = 'cluster4_markers_immature_umapl_expr_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 4, height = 1, dpi = 150)

jy_immature.markers <- FindMarkers(jy_immature, ident.1 = 3, ident.2 = 4, only.pos = FALSE)

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markers2 = jy_immature.markers %>%
   slice_max(n = 8, order_by = avg_log2FC)
markers2

clusters = as.numeric(sort(unique(jy_408$unified_clusters)))
plots <- lapply(1:length(clusters), function(i){
    plot_clusters_vertical_spatial(jy_408, cluster = clusters[i], pt.size = 1, clustering = 'unified_clusters', anterior = FALSE)
  })

Error in plot_clusters_vertical_spatial(jy_408, cluster = clusters[i],  : 
  could not find function "plot_clusters_vertical_spatial"

plot_clusters_vertical_spatial <- function(sobj, cluster, clustering = NULL, anterior = FALSE, cluster_color =  '#CB2A55', pt.size = 1, space = "H", arc = TRUE)
{
  cluster_identity = as.numeric(unlist(ifelse(is.null(clustering),
                                              Idents(sobj) == levels(Idents(sobj))[cluster],sobj[[clustering]]))) == (cluster)
  coordinates <- Embeddings(sobj, reduction = space)
  gene_df <- as.data.frame(cbind(coordinates, cluster_identity))
  colnames(gene_df) <- c('X', 'Y', 'clust')
  gene_df <- gene_df %>% dplyr::arrange(clust)
  plot <- ggplot(gene_df, aes(x = X, y = Y, color = factor(clust))) + geom_point(size = pt.size, alpha = 1) +  
            theme_classic() + ggtitle(cluster) + NoAxes() + NoLegend() + 
    coord_fixed(ratio = 0.5)  + theme(title = element_text(face = 'bold', size = rel(0.8), hjust = 1)) 
  cluster_color = scales::hue_pal()(nrow(unique(sobj[[clustering]])))[cluster]
  plot = plot + scale_colour_manual(values = c('grey90', cluster_color))
  intercept = ifelse(anterior, 660, 484)
  if(arc){plot = plot + geom_hline(yintercept=484, linetype = "dashed",color = cluster_color)}
  return(plot)
}
plot_clusters_vertical_spatial(jy_164, pt.size = 1, cluster = 3, clustering = 'RNA_snn_res.0.8')

plot_features_vertical_spatial_smoothed <- function(sobj, gene, pt.size = 0.5, space = "H", arc = TRUE)
{
  coordinates <- Embeddings(sobj, reduction = space)
  expmat <- as.matrix(FetchData(sobj, gene))
  gene_df <- as.data.frame(cbind(coordinates, expmat))
  colnames(gene_df) <- c('X', 'Y', 'expr')
  gene_df <- gene_df %>% dplyr::arrange(!is.na(expr), expr)
  colors = c('grey90', 'grey90', '#0f4c5c')
  gene_df$expr[gene_df$expr == 0] = NA
  plot <- gene_df %>%
    filter(!is.na(expr)) %>%
    ggplot(aes(x = X, y = Y, color = expr)) +stat_density_2d(aes(fill = ..density..), geom = "raster", n = 400,contour = FALSE, interpolate = TRUE) +
  scale_x_continuous(expand = c(0, 0)) +
  scale_y_continuous(expand = c(0, 0)) +
#geom_bin2d(bins = 10) + #geom_point(size = pt.size, alpha = 1)+  
            theme_classic() + ggtitle(gene) + NoAxes() + NoLegend() + 
    coord_fixed(ratio = 0.5) + scale_fill_gradient(na.value = colors[1], low = colors[2], high = colors[3], labels = NULL)  + theme(title = element_text(face = 'bold', size = rel(0.5), hjust = 1)) 
  if(arc){plot = plot + geom_hline(yintercept=660, linetype = "dashed",color = colors[3])}
  return(plot)
}
plot_features_vertical_spatial_smoothed(jy_164, gene = 'PAX6')

genes = rownames(jy_408)
plots <- lapply(1:length(genes), function(i){
    plot_features_vertical_spatial_smoothed(jy_408, genes[i], pt.size = 1)
  })
verts= plot_grid(plotlist = plots, label_size = 10, nrow = 1)
verts

ggsave(plot = verts, filename = 'test_408_smoothed-vertical_expr_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 18, height = 8, dpi = 150)

normed_data <- GetAssayData(jy_all, slot = 'data')
gad_1_true = normed_data['GAD1', ] != 0
jy_all$gad1 = gad_1_true
jy_gad = jy_all[, jy_all$gad1]


breakpoints = 1:20/10+0.3
plots = list()
jy_gad <- FindVariableFeatures(jy_gad, selection.method = "vst")

Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

all.genes <- rownames(jy_gad)
jy_gad <- ScaleData(jy_gad, features = all.genes)

Centering and scaling data matrix

  |                                                                                                                                                                           
  |                                                                                                                                                                     |   0%
  |                                                                                                                                                                           
  |=====================================================================================================================================================================| 100%

jy_gad <- FindNeighbors(jy_gad, dims = 1:30)

Computing nearest neighbor graph
Computing SNN

i = 1
for (breakpoint in breakpoints){
  jy_gad <- FindClusters(jy_gad, resolution = breakpoint)
  jy_gad <- RunUMAP(jy_gad, dims = 1:30)
  jy_gad.markers <- FindAllMarkers(jy_gad, only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25)
  labels = jy_gad.markers %>%
   group_by(cluster) %>%
   slice_max(n = 1, order_by = avg_log2FC)
  new.cluster.ids <- labels$gene
  names(new.cluster.ids) <- levels(jy_gad)
  jy_gad <- RenameIdents(jy_gad, new.cluster.ids)
  plots[[i]] = DimPlot(jy_gad, reduction = "umap", pt.size = 1, label = TRUE) + NoAxes() + NoLegend() + ggtitle(breakpoint)
  i = i + 1
}

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.7572
Number of communities: 5
Elapsed time: 0 seconds

13:03:06 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:06 Read 1137 rows and found 30 numeric columns
13:03:06 Using Annoy for neighbor search, n_neighbors = 30
13:03:06 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:06 Writing NN index file to temp file /tmp/RtmpfJenoj/file767657dabb5f1
13:03:06 Searching Annoy index using 1 thread, search_k = 3000
13:03:06 Annoy recall = 100%
13:03:06 Commencing smooth kNN distance calibration using 1 thread
13:03:07 Initializing from normalized Laplacian + noise
13:03:07 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:08 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++                                               | 6 % ~00s          
  |++++++                                            | 11% ~00s          
  |+++++++++                                         | 17% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |++++++++++++++                                    | 28% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |++++++++++++++++++++                              | 39% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |+++++++++++++++++++++++++++++++                   | 61% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 72% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++  | 94% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.7338
Number of communities: 6
Elapsed time: 0 seconds

13:03:09 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:09 Read 1137 rows and found 30 numeric columns
13:03:09 Using Annoy for neighbor search, n_neighbors = 30
13:03:09 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:09 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765529e9362
13:03:09 Searching Annoy index using 1 thread, search_k = 3000
13:03:09 Annoy recall = 100%
13:03:10 Commencing smooth kNN distance calibration using 1 thread
13:03:10 Initializing from normalized Laplacian + noise
13:03:10 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:12 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |+++++++                                           | 13% ~00s          
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++                          | 47% ~00s          
  |+++++++++++++++++++++++++++                       | 53% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 87% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.7155
Number of communities: 7
Elapsed time: 0 seconds

13:03:12 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:12 Read 1137 rows and found 30 numeric columns
13:03:12 Using Annoy for neighbor search, n_neighbors = 30
13:03:12 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:12 Writing NN index file to temp file /tmp/RtmpfJenoj/file767656f6088aa
13:03:12 Searching Annoy index using 1 thread, search_k = 3000
13:03:13 Annoy recall = 100%
13:03:13 Commencing smooth kNN distance calibration using 1 thread
13:03:14 Initializing from normalized Laplacian + noise
13:03:14 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:15 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6971
Number of communities: 7
Elapsed time: 0 seconds

13:03:16 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:16 Read 1137 rows and found 30 numeric columns
13:03:16 Using Annoy for neighbor search, n_neighbors = 30
13:03:16 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:16 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765cdbea8b
13:03:16 Searching Annoy index using 1 thread, search_k = 3000
13:03:16 Annoy recall = 100%
13:03:17 Commencing smooth kNN distance calibration using 1 thread
13:03:17 Initializing from normalized Laplacian + noise
13:03:17 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:19 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6796
Number of communities: 8
Elapsed time: 0 seconds

13:03:19 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:19 Read 1137 rows and found 30 numeric columns
13:03:19 Using Annoy for neighbor search, n_neighbors = 30
13:03:19 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:19 Writing NN index file to temp file /tmp/RtmpfJenoj/file7676569b8b375
13:03:19 Searching Annoy index using 1 thread, search_k = 3000
13:03:20 Annoy recall = 100%
13:03:20 Commencing smooth kNN distance calibration using 1 thread
13:03:21 Initializing from normalized Laplacian + noise
13:03:21 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:22 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6643
Number of communities: 9
Elapsed time: 0 seconds

13:03:23 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:23 Read 1137 rows and found 30 numeric columns
13:03:23 Using Annoy for neighbor search, n_neighbors = 30
13:03:23 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:23 Writing NN index file to temp file /tmp/RtmpfJenoj/file767657dc91999
13:03:23 Searching Annoy index using 1 thread, search_k = 3000
13:03:23 Annoy recall = 100%
13:03:24 Commencing smooth kNN distance calibration using 1 thread
13:03:24 Initializing from normalized Laplacian + noise
13:03:24 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:26 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6502
Number of communities: 9
Elapsed time: 0 seconds

13:03:26 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:26 Read 1137 rows and found 30 numeric columns
13:03:26 Using Annoy for neighbor search, n_neighbors = 30
13:03:26 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:26 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765b780f30
13:03:26 Searching Annoy index using 1 thread, search_k = 3000
13:03:27 Annoy recall = 100%
13:03:27 Commencing smooth kNN distance calibration using 1 thread
13:03:28 Initializing from normalized Laplacian + noise
13:03:28 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:29 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6350
Number of communities: 10
Elapsed time: 0 seconds

13:03:30 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:30 Read 1137 rows and found 30 numeric columns
13:03:30 Using Annoy for neighbor search, n_neighbors = 30
13:03:30 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:30 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765231577fc
13:03:30 Searching Annoy index using 1 thread, search_k = 3000
13:03:30 Annoy recall = 100%
13:03:31 Commencing smooth kNN distance calibration using 1 thread
13:03:32 Initializing from normalized Laplacian + noise
13:03:32 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:33 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |++++                                              | 6 % ~00s          
  |+++++++                                           | 12% ~00s          
  |++++++++++                                        | 19% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |++++++++++++++++++++++                            | 44% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 56% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 81% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 94% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6222
Number of communities: 10
Elapsed time: 0 seconds

13:03:34 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:34 Read 1137 rows and found 30 numeric columns
13:03:34 Using Annoy for neighbor search, n_neighbors = 30
13:03:34 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:34 Writing NN index file to temp file /tmp/RtmpfJenoj/file7676513ea33a3
13:03:34 Searching Annoy index using 1 thread, search_k = 3000
13:03:34 Annoy recall = 100%
13:03:34 Commencing smooth kNN distance calibration using 1 thread
13:03:35 Initializing from normalized Laplacian + noise
13:03:35 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:37 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.6108
Number of communities: 11
Elapsed time: 0 seconds

13:03:37 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:37 Read 1137 rows and found 30 numeric columns
13:03:37 Using Annoy for neighbor search, n_neighbors = 30
13:03:37 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:38 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765258e0317
13:03:38 Searching Annoy index using 1 thread, search_k = 3000
13:03:38 Annoy recall = 100%
13:03:38 Commencing smooth kNN distance calibration using 1 thread
13:03:39 Initializing from normalized Laplacian + noise
13:03:39 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:40 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5994
Number of communities: 11
Elapsed time: 0 seconds

13:03:41 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:41 Read 1137 rows and found 30 numeric columns
13:03:41 Using Annoy for neighbor search, n_neighbors = 30
13:03:41 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:41 Writing NN index file to temp file /tmp/RtmpfJenoj/file767652cf034bd
13:03:41 Searching Annoy index using 1 thread, search_k = 3000
13:03:42 Annoy recall = 100%
13:03:42 Commencing smooth kNN distance calibration using 1 thread
13:03:43 Initializing from normalized Laplacian + noise
13:03:43 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:44 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~00s          
  |++++++++                                          | 15% ~00s          
  |++++++++++++                                      | 23% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |++++++++++++++++++++                              | 38% ~00s          
  |++++++++++++++++++++++++                          | 46% ~00s          
  |+++++++++++++++++++++++++++                       | 54% ~00s          
  |+++++++++++++++++++++++++++++++                   | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 77% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5885
Number of communities: 12
Elapsed time: 0 seconds

13:03:45 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:45 Read 1137 rows and found 30 numeric columns
13:03:45 Using Annoy for neighbor search, n_neighbors = 30
13:03:45 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:45 Writing NN index file to temp file /tmp/RtmpfJenoj/file7676560fe697
13:03:45 Searching Annoy index using 1 thread, search_k = 3000
13:03:45 Annoy recall = 100%
13:03:46 Commencing smooth kNN distance calibration using 1 thread
13:03:46 Initializing from normalized Laplacian + noise
13:03:46 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:48 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5778
Number of communities: 12
Elapsed time: 0 seconds

13:03:49 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:49 Read 1137 rows and found 30 numeric columns
13:03:49 Using Annoy for neighbor search, n_neighbors = 30
13:03:49 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:49 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765173b0aa1
13:03:49 Searching Annoy index using 1 thread, search_k = 3000
13:03:49 Annoy recall = 100%
13:03:50 Commencing smooth kNN distance calibration using 1 thread
13:03:50 Initializing from normalized Laplacian + noise
13:03:50 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:52 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5666
Number of communities: 12
Elapsed time: 0 seconds

13:03:53 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:53 Read 1137 rows and found 30 numeric columns
13:03:53 Using Annoy for neighbor search, n_neighbors = 30
13:03:53 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:53 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765488c0a9
13:03:53 Searching Annoy index using 1 thread, search_k = 3000
13:03:53 Annoy recall = 100%
13:03:53 Commencing smooth kNN distance calibration using 1 thread
13:03:54 Initializing from normalized Laplacian + noise
13:03:54 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:55 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5566
Number of communities: 13
Elapsed time: 0 seconds

13:03:56 UMAP embedding parameters a = 0.9922 b = 1.112
13:03:56 Read 1137 rows and found 30 numeric columns
13:03:56 Using Annoy for neighbor search, n_neighbors = 30
13:03:56 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:57 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765e0cede1
13:03:57 Searching Annoy index using 1 thread, search_k = 3000
13:03:57 Annoy recall = 100%
13:03:57 Commencing smooth kNN distance calibration using 1 thread
13:03:58 Initializing from normalized Laplacian + noise
13:03:58 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:03:59 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |++++++++                                          | 14% ~00s          
  |+++++++++++                                       | 21% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++                                | 36% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |+++++++++++++++++++++++++++++++++                 | 64% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 79% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 12

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5465
Number of communities: 13
Elapsed time: 0 seconds

13:04:00 UMAP embedding parameters a = 0.9922 b = 1.112
13:04:00 Read 1137 rows and found 30 numeric columns
13:04:00 Using Annoy for neighbor search, n_neighbors = 30
13:04:00 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:00 Writing NN index file to temp file /tmp/RtmpfJenoj/file76765623ef3bd
13:04:00 Searching Annoy index using 1 thread, search_k = 3000
13:04:01 Annoy recall = 100%
13:04:01 Commencing smooth kNN distance calibration using 1 thread
13:04:02 Initializing from normalized Laplacian + noise
13:04:02 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:03 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |+++++++                                           | 13% ~00s          
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++                          | 47% ~00s          
  |+++++++++++++++++++++++++++                       | 53% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 87% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 12

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5364
Number of communities: 14
Elapsed time: 0 seconds

13:04:04 UMAP embedding parameters a = 0.9922 b = 1.112
13:04:04 Read 1137 rows and found 30 numeric columns
13:04:04 Using Annoy for neighbor search, n_neighbors = 30
13:04:04 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:04 Writing NN index file to temp file /tmp/RtmpfJenoj/file767657373bc63
13:04:04 Searching Annoy index using 1 thread, search_k = 3000
13:04:05 Annoy recall = 100%
13:04:05 Commencing smooth kNN distance calibration using 1 thread
13:04:06 Initializing from normalized Laplacian + noise
13:04:06 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:07 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |++++                                              | 7 % ~00s          
  |+++++++                                           | 13% ~00s          
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++                          | 47% ~00s          
  |+++++++++++++++++++++++++++                       | 53% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 87% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 93% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 12

  |                                                  | 0 % ~calculating  
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 13

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5275
Number of communities: 15
Elapsed time: 0 seconds

13:04:08 UMAP embedding parameters a = 0.9922 b = 1.112
13:04:08 Read 1137 rows and found 30 numeric columns
13:04:08 Using Annoy for neighbor search, n_neighbors = 30
13:04:08 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:08 Writing NN index file to temp file /tmp/RtmpfJenoj/file767655f8a538b
13:04:08 Searching Annoy index using 1 thread, search_k = 3000
13:04:08 Annoy recall = 100%
13:04:09 Commencing smooth kNN distance calibration using 1 thread
13:04:10 Initializing from normalized Laplacian + noise
13:04:10 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:11 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |++++                                              | 6 % ~00s          
  |+++++++                                           | 12% ~00s          
  |++++++++++                                        | 19% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |++++++++++++++++++++++                            | 44% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 56% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 81% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 94% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 12

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 13

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 14

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5186
Number of communities: 16
Elapsed time: 0 seconds

13:04:12 UMAP embedding parameters a = 0.9922 b = 1.112
13:04:12 Read 1137 rows and found 30 numeric columns
13:04:12 Using Annoy for neighbor search, n_neighbors = 30
13:04:12 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:12 Writing NN index file to temp file /tmp/RtmpfJenoj/file767656782cb10
13:04:12 Searching Annoy index using 1 thread, search_k = 3000
13:04:12 Annoy recall = 100%
13:04:13 Commencing smooth kNN distance calibration using 1 thread
13:04:14 Initializing from normalized Laplacian + noise
13:04:14 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:15 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |++++                                              | 6 % ~00s          
  |+++++++                                           | 12% ~00s          
  |++++++++++                                        | 19% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |++++++++++++++++++++++                            | 44% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 56% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 69% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 81% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 94% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 9

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 10

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 11

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 12

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 13

  |                                                  | 0 % ~calculating  
  |+++++                                             | 8 % ~00s          
  |+++++++++                                         | 17% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++                             | 42% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 58% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 14

  |                                                  | 0 % ~calculating  
  |++++++++++                                        | 20% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 15

  |                                                  | 0 % ~calculating  
  |++++++                                            | 11% ~00s          
  |++++++++++++                                      | 22% ~00s          
  |+++++++++++++++++                                 | 33% ~00s          
  |+++++++++++++++++++++++                           | 44% ~00s          
  |++++++++++++++++++++++++++++                      | 56% ~00s          
  |++++++++++++++++++++++++++++++++++                | 67% ~00s          
  |+++++++++++++++++++++++++++++++++++++++           | 78% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 89% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1137
Number of edges: 39738

Running Louvain algorithm...

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Maximum modularity in 10 random starts: 0.5097
Number of communities: 16
Elapsed time: 0 seconds

13:04:16 UMAP embedding parameters a = 0.9922 b = 1.112
13:04:16 Read 1137 rows and found 30 numeric columns
13:04:16 Using Annoy for neighbor search, n_neighbors = 30
13:04:16 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:16 Writing NN index file to temp file /tmp/RtmpfJenoj/file7676567fec782
13:04:16 Searching Annoy index using 1 thread, search_k = 3000
13:04:17 Annoy recall = 100%
13:04:17 Commencing smooth kNN distance calibration using 1 thread
13:04:18 Initializing from normalized Laplacian + noise
13:04:18 Commencing optimization for 500 epochs, with 43072 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
13:04:19 Optimization finished
Calculating cluster 0

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 1

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 2

  |                                                  | 0 % ~calculating  
  |+++++                                             | 10% ~00s          
  |++++++++++                                        | 20% ~00s          
  |+++++++++++++++                                   | 30% ~00s          
  |++++++++++++++++++++                              | 40% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++                    | 60% ~00s          
  |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
  |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 3

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 4

  |                                                  | 0 % ~calculating  
  |+++++++                                           | 12% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++                  | 62% ~00s          
  |++++++++++++++++++++++++++++++++++++++            | 75% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++      | 88% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 5

  |                                                  | 0 % ~calculating  
  |++++++++                                          | 14% ~00s          
  |+++++++++++++++                                   | 29% ~00s          
  |++++++++++++++++++++++                            | 43% ~00s          
  |+++++++++++++++++++++++++++++                     | 57% ~00s          
  |++++++++++++++++++++++++++++++++++++              | 71% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 6

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 7

  |                                                  | 0 % ~calculating  
  |+++++                                             | 9 % ~00s          
  |++++++++++                                        | 18% ~00s          
  |++++++++++++++                                    | 27% ~00s          
  |+++++++++++++++++++                               | 36% ~00s          
  |+++++++++++++++++++++++                           | 45% ~00s          
  |++++++++++++++++++++++++++++                      | 55% ~00s          
  |++++++++++++++++++++++++++++++++                  | 64% ~00s          
  |+++++++++++++++++++++++++++++++++++++             | 73% ~00s          
  |+++++++++++++++++++++++++++++++++++++++++         | 82% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  

Calculating cluster 8

  |                                                  | 0 % ~calculating  
  |++++                                              | 6 % ~00s          
  |+++++++                                           | 12% ~00s          
  |++++++++++                                        | 19% ~00s          
  |+++++++++++++                                     | 25% ~00s          
  |++++++++++++++++                                  | 31% ~00s          
  |+++++++++++++++++++                               | 38% ~00s          
  |++++++++++++++++++++++                            | 44% ~00s          
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |+++++++++++++++++++++++++++++                     | 56% ~00s          
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Calculating cluster 9

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Calculating cluster 13

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marrangeGrob(plots, nrow=2, ncol=2)

ml <- marrangeGrob(plots, nrow=2, ncol=2)
ggsave(filename = 'gad1_sequential_clustering_umaps.pdf', path = file.path(output_dir_plot, '20220721_1'), ml)

Saving 7.29 x 4.5 in image

genes = rownames(jy_gad)
plots <- lapply(1:length(genes), function(i){
    plot_features_umap(jy_gad, genes[i], pt.size = 0.5)
  })
umaps = plot_grid(plotlist = plots, label_size = 10, nrow = 4)
umaps

#ggsave(plot = umaps, filename = 'test_immature_umapl_expr_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 10, height = 4, dpi = 150)

big_dimplot <- function(sobj, grep_pattern){
  dp = DimPlot(sobj, cells.highlight = list(imp = which(grepl(grep_pattern, sobj$area))))
  dp <- dp + scale_color_manual(values = c('grey90', '#1982c4'), labels=c('other', grep_pattern)) + NoAxes()
}
patterns = c('408_CC', '408_MS_CC', 'vMS_TC', 'dMS_TC', '408_TC', '164_CC', '164_MS_CC', '164_MS_TC',  '164_TC')
plots <- lapply(1:length(patterns), function(i){
    big_dimplot(jy_gad, grep_pattern = patterns[i])
  })

Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.

areas = plot_grid(plotlist = plots, label_size = 10, nrow = 3)
areas

ggsave(plot = areas, filename = 'test_gad_area_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 14, height = 8, dpi = 150)

plot_vertical_smoothed <- function(sobj, gene, images_ordered){
  expmat <- as.matrix(FetchData(sobj, gene))
  ## What's the logic. I need to build a rectangle, so just give it the x, y
  ## and fill is not density
  xpos = rep(0, length(images_ordered))
  ypos = 1:length(images_ordered)
  image_expr = c()
  for(i in 1:length(images_ordered)){
    image = images_ordered[i]
    gene_expr_in_subset = expmat[sobj$IMAGE.NAME == image]
    image_expr = c(image_expr, mean(gene_expr_in_subset))
  }
  tile_df = as.data.frame(cbind(xpos, ypos, image_expr)) 
  colnames(tile_df) <-  c('X', 'Y','mean_expr')
  p <- tile_df %>%
    ggplot(aes(x = X, y = Y, fill = mean_expr)) + geom_raster(interpolate = TRUE) +
    coord_fixed() + theme_classic() + NoAxes() + NoLegend() + ggtitle(gene) + theme(title = element_text(face = 'bold', size = rel(0.5), hjust = 1)) 
  return(p)
}

plot_vertical_smoothed(jy_164, 'PAX6', images_ordered)

genes_to_show = c('DCX', 'GAD1', 'DLX2', 'NKX2.1', 'PROX1', 'MAF1', 'TSHZ1', 'CXCR4', 'CXCL12', 'CALB2', 'TBR1')
genes = genes_to_show
plots <- lapply(1:length(genes), function(i){
    plot_vertical_smoothed(jy_164, genes[i], images_ordered)
  })
verts= plot_grid(plotlist = plots, label_size = 10, nrow = 1)
verts
#ggsave(plot = verts, filename = 'test_408_smoothed-vertical_expr_plots_size1_alpha1.png', path = file.path(output_dir_plot, '20220721_1'), width = 18, height = 8, dpi = 150)

rplot <- RidgePlot(jy_all, features = genes_to_show, group.by = 'area', ncol = 2)
ggsave(rplot, filename = 'rplot_by_area.png', path = file.path(output_dir_plot, '20220727_1'), width = 6, height = 15, dpi = 150)

Picking joint bandwidth of 0.283
Picking joint bandwidth of 1.05
Picking joint bandwidth of 0.896
Picking joint bandwidth of 1.14
Picking joint bandwidth of 0.774
Picking joint bandwidth of 0.472
Picking joint bandwidth of 0.845
Picking joint bandwidth of 0.918
Picking joint bandwidth of 1.02
Picking joint bandwidth of 0.973
Picking joint bandwidth of 0.955

vplot <- VlnPlot(jy_all, features = genes_to_show, group.by = 'area', ncol = 3)
vplot
ggsave(vplot, filename = 'vplot_by_area.png', path = file.path(output_dir_plot, '20220727_1'), width = 10, height = 15, dpi = 150)

vplot <- VlnPlot(jy_all, features = genes_to_show, group.by = 'area', ncol = 3)
vplot
ggsave(vplot, filename = 'vplot_by_area.png', path = file.path(output_dir_plot, '20220727_1'), width = 10, height = 15, dpi = 150)

genes_to_show = c('DCX', 'GAD1', 'CXCR4', 'DLX2', 'NKX2.1', 'PROX1', 'MAF1', 'TSHZ1', 'CXCL12', 'CALB2', 'TBR1', 'COUPTF2', 'SP8', 'SCGN')
dplot <- DotPlot(jy_all, features = genes_to_show, group.by = 'broad_areas',) + RotatedAxis() + coord_flip()
dplot

#ggsave(dplot, filename = 'dplot_by_broadarea_allgenes.png', path = file.path(output_dir_plot, '20220727_1'), width = 9, height = 3, dpi = 150)

broad_areas = c()
jy_all$broad_areas = 'wrong'
jy_all$broad_areas[grepl('408', jy_all$area) & grepl('TC', jy_all$area)] = 'pVentral'
jy_all$broad_areas[grepl('408', jy_all$area) & grepl('CC', jy_all$area)] = 'pDorsal'
jy_all$broad_areas[grepl('164', jy_all$area) & grepl('TC', jy_all$area)] = 'aVentral'
jy_all$broad_areas[grepl('164', jy_all$area) & grepl('CC', jy_all$area)] = 'aDorsal'

big_dimplot <- function(sobj, grep_pattern){
  dp = DimPlot(sobj, cells.highlight = list(imp = which(grepl(grep_pattern, sobj$broad_areas))))
  dp <- dp + scale_color_manual(values = c('grey90', '#1982c4'), labels=c('other', grep_pattern)) + NoAxes()
}
patterns = c('AntDrs', 'AntVnt', 'PosDrs', 'PosVnt')
plots <- lapply(1:length(patterns), function(i){
    big_dimplot(jy_all, grep_pattern = patterns[i])
  })

Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.

areas = plot_grid(plotlist = plots, label_size = 10, nrow = 3)
areas

ggsave(plot = areas, filename = 'umap_broad_areas.png', path = file.path(output_dir_plot, '20220727_1'), width = 10, height = 8, dpi = 150)